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Miranda-Galvis M, Carneiro Soares C, Moretto Carnielli C, Ramalho Buttura J, Sales de Sá R, Kaminagakura E, Marchi FA, Paes Leme AF, Lópes Pinto CA, Santos-Silva AR, Moraes Castilho R, Kowalski LP, Squarize CH. New Insights into the Impact of Human Papillomavirus on Oral Cancer in Young Patients: Proteomic Approach Reveals a Novel Role for S100A8. Cells 2023; 12:cells12091323. [PMID: 37174723 PMCID: PMC10177374 DOI: 10.3390/cells12091323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Human papillomavirus (HPV) infection has recently been linked to a subset of cancers affecting the oral cavity. However, the molecular mechanisms underlying HPV-driven oral squamous cell carcinoma (OSCC) onset and progression are poorly understood. METHODS We performed MS-based proteomics profiling based on HPV status in OSCC in young patients, following biological characterization and cell assays to explore the proteome functional landscape. RESULTS Thirty-nine proteins are differentially abundant between HPV (+) and HPV (-) OSCC. Among them, COPS3, DYHC1, and S100A8 are unfavorable for tumor recurrence and survival, in contrast to A2M and Serpine1, low levels of which show an association with better DFS. Remarkably, S100A8 is considered an independent prognostic factor for lower survival rates, and at high levels, it alters tumor-associated immune profiling, showing a lower proportion of M1 macrophages and dendritic cells. HPV (+) OSCC also displayed the pathogen-associated patterns receptor that, when activated, triggered the S100A8 and NFκB inflammatory responses. CONCLUSION HPV (+) OSCC has a peculiar microenvironment pattern distinctive from HPV (-), involving the expression of pathogen-associated pattern receptors, S100A8 overexpression, and NFκB activation and responses, which has important consequences in prognosis and may guide therapeutic decisions.
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Affiliation(s)
- Marisol Miranda-Galvis
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Carolina Carneiro Soares
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
- Department of Microbiology, Immune Biology, and Genetics, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
| | - Carolina Moretto Carnielli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Jaqueline Ramalho Buttura
- Laboratory of Bioinformatics and Computational Biology, A.C.Camargo Cancer Center (CIPE), São Paulo 01508-010, SP, Brazil
| | - Raisa Sales de Sá
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Estela Kaminagakura
- Department of Bioscience and Oral Diagnosis, Science and Technology Institute, University of São Paulo State (UNESP), São José dos Campos 01049-010, SP, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, SP, Brazil
- Comprehensive Center for Precision Oncology, University of São Paulo, São Paulo 05508-900, SP, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Clóvis A Lópes Pinto
- Department of Anatomic Pathology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Rogerio Moraes Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Luiz Paulo Kowalski
- Head and Neck Surgery Department, Medical School, University of São Paulo, São Paulo 05508-900, SP, Brazil
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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Suchanti S, Stephen BJ, Awasthi S, Awasthi SK, Singh G, Singh A, Mishra R. Harnessing the role of epigenetic histone modification in targeting head and neck squamous cell carcinoma. Epigenomics 2022; 14:279-293. [PMID: 35184601 DOI: 10.2217/epi-2020-0348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent form of cancer worldwide. Despite advancements made in treatment strategies, the fatality rate of HNSCC is very high. An accumulating body of evidence suggests that epigenetic modification of histones plays an influential role in the development and progression of the disease. In this review we discuss the role of epigenetic modifications in HNSCC and the inter-relationships of human papillomavirus oncoproteins and histone-modifying agents. Further, we explore the possibility of identifying these modifications as biomarkers for their use as drugs in treatment strategies.
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Affiliation(s)
- Surabhi Suchanti
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Bjorn J Stephen
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Sonali Awasthi
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, 208024, India
| | - Sudhir K Awasthi
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, 208024, India
| | - Gyanendra Singh
- Toxicology Division, ICMR-National Institute of Occupational Health, Ahmedabad, Gujarat, 380016, India
| | - Abhijeet Singh
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Rajeev Mishra
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh, 208024, India
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Eggeling F, Hoffmann F. Microdissection—An Essential Prerequisite for Spatial Cancer Omics. Proteomics 2020; 20:e2000077. [DOI: 10.1002/pmic.202000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ferdinand Eggeling
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
| | - Franziska Hoffmann
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
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Wang K, Yu XH, Tang YJ, Tang YL, Liang XH. Obesity: An emerging driver of head and neck cancer. Life Sci 2019; 233:116687. [PMID: 31348948 DOI: 10.1016/j.lfs.2019.116687] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 02/05/2023]
Abstract
Obesity has become pandemic and emerged as one of the most critical global health care problems worldwide since last century. Recent studies have demonstrated that there may be a causal link between obesity and higher risks and mortality of cancers, including prostate, breast, colon, and thyroid cancers, head and neck cancer (HNC). This review focuses on the relationship between obesity and HNC, and the molecular mechanism of abnormal lipid metabolism in HNC. Elucidating the mechanism may open up new possibilities for strategies to reduce risk and mortality of HNC in an increasingly obese population.
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Affiliation(s)
- Ke Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Oral And Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xiang-Hua Yu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Oral And Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
| | - Ya-Ling Tang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Oral Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Xin-Hua Liang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Oral And Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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Chen X, Mims J, Huang X, Singh N, Motea E, Planchon SM, Beg M, Tsang AW, Porosnicu M, Kemp ML, Boothman DA, Furdui CM. Modulators of Redox Metabolism in Head and Neck Cancer. Antioxid Redox Signal 2018; 29:1660-1690. [PMID: 29113454 PMCID: PMC6207163 DOI: 10.1089/ars.2017.7423] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Head and neck squamous cell cancer (HNSCC) is a complex disease characterized by high genetic and metabolic heterogeneity. Radiation therapy (RT) alone or combined with systemic chemotherapy is widely used for treatment of HNSCC as definitive treatment or as adjuvant treatment after surgery. Antibodies against epidermal growth factor receptor are used in definitive or palliative treatment. Recent Advances: Emerging targeted therapies against other proteins of interest as well as programmed cell death protein 1 and programmed death-ligand 1 immunotherapies are being explored in clinical trials. CRITICAL ISSUES The disease heterogeneity, invasiveness, and resistance to standard of care RT or chemoradiation therapy continue to constitute significant roadblocks for treatment and patients' quality of life (QOL) despite improvements in treatment modality and the emergence of new therapies over the past two decades. FUTURE DIRECTIONS As reviewed here, alterations in redox metabolism occur at all stages of HNSCC management, providing opportunities for improved prevention, early detection, response to therapies, and QOL. Bioinformatics and computational systems biology approaches are key to integrate redox effects with multiomics data from cells and clinical specimens and to identify redox modifiers or modifiable target proteins to achieve improved clinical outcomes. Antioxid. Redox Signal.
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Affiliation(s)
- Xiaofei Chen
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Jade Mims
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Xiumei Huang
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Naveen Singh
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Edward Motea
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | | | - Muhammad Beg
- Department of Internal Medicine, Division of Hematology-Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - Allen W. Tsang
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Mercedes Porosnicu
- Department of Internal Medicine, Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Melissa L. Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - David A. Boothman
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
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Vidotto A, Polachini GM, de Paula-Silva M, Oliani SM, Henrique T, López RVM, Cury PM, Nunes FD, Góis-Filho JF, de Carvalho MB, Leopoldino AM, Tajara EH. Differentially expressed proteins in positive versus negative HNSCC lymph nodes. BMC Med Genomics 2018; 11:73. [PMID: 30157864 PMCID: PMC6114741 DOI: 10.1186/s12920-018-0382-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/02/2018] [Indexed: 12/21/2022] Open
Abstract
Background Lymph node metastasis is one of the most important prognostic factors in head and neck squamous cell carcinomas (HNSCCs) and critical for delineating their treatment. However, clinical and histological criteria for the diagnosis of nodal status remain limited. In the present study, we aimed to characterize the proteomic profile of lymph node metastasis from HNSCC patients. Methods In the present study, we used one- and two-dimensional electrophoresis and mass spectrometry analysis to characterize the proteomic profile of lymph node metastasis from HNSCC. Results Comparison of metastatic and non-metastatic lymph nodes showed 52 differentially expressed proteins associated with neoplastic development and progression. The results reinforced the idea that tumors from different anatomical subsites have dissimilar behaviors, which may be influenced by micro-environmental factor including the lymphatic network. The expression pattern of heat shock proteins and glycolytic enzymes also suggested an effect of the lymph node environment in controlling tumor growth or in metabolic reprogramming of the metastatic cell. Our study, for the first time, provided direct evidence of annexin A1 overexpression in lymph node metastasis of head and neck cancer, adding information that may be useful for diagnosing aggressive disease. Conclusions In brief, this study contributed to our understanding of the metastatic phenotype of HNSCC and provided potential targets for diagnostic in this group of carcinomas. Electronic supplementary material The online version of this article (10.1186/s12920-018-0382-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessandra Vidotto
- Departamento de Biologia Molecular, Faculdade de Medicina (FAMERP), Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Giovana M Polachini
- Departamento de Biologia Molecular, Faculdade de Medicina (FAMERP), Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Marina de Paula-Silva
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (UNESP), R. Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP 15054-000, Brazil
| | - Sonia M Oliani
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (UNESP), R. Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP 15054-000, Brazil
| | - Tiago Henrique
- Departamento de Biologia Molecular, Faculdade de Medicina (FAMERP), Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil
| | - Rossana V M López
- Instituto do Câncer de São Paulo Octavio Frias de Oliveira - ICESP, Av. Dr. Arnaldo, 251 - Cerqueira César, São Paulo, SP, CEP 01246-000, Brazil
| | - Patrícia M Cury
- Faculdade Ceres (Faceres), Av. Anísio Haddad, 6751, São José do Rio Preto, SP, CEP 15090-305, Brazil
| | - Fabio D Nunes
- Departamento de Estomatologia, Faculdade de Odontologia, Universidade de São Paulo, Av. Prof. Lineu Prestes, 2227, São Paulo, SP, CEP 05508-000, Brazil
| | - José F Góis-Filho
- Instituto do Câncer Arnaldo Vieira de Carvalho, R. Dr Cesário Mota Jr, 112, São Paulo, SP, CEP 01221-020, Brazil
| | - Marcos B de Carvalho
- Departamento de Cirurgia de Cabeça e Pescoço, Hospital Heliópolis, R. Cônego Xavier, 276, São Paulo, SP, CEP 04231-030, Brazil
| | - Andréia M Leopoldino
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café, s/n, Ribeirão Preto, SP, CEP 14040-903, Brazil
| | - Eloiza H Tajara
- Departamento de Biologia Molecular, Faculdade de Medicina (FAMERP), Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, SP, CEP 15090-000, Brazil. .,Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, R. do Matão, 321, São Paulo, SP, CEP 05508-090, Brazil.
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Chen X, Zhao Y. Human papillomavirus infection in oral potentially malignant disorders and cancer. Arch Oral Biol 2017; 83:334-339. [PMID: 28886585 DOI: 10.1016/j.archoralbio.2017.08.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/21/2017] [Accepted: 08/21/2017] [Indexed: 12/18/2022]
Abstract
Human papillomavirus (HPV) infects keratinocytes in the mucosa or skin, and persistent infection with HPV may lead to premalignant lesions and invasive cancer, especially cervical cancer. It has also been hypothesized that HPV infection is an etiological factor of oral squamous cell carcinoma and oral precancerous disorders such as lichen planus, leukoplakia, and erythroplakia. A high percentage of HPV in oral lesions supports the possible viral contribution, but an association of HPV infection with these lesions remains to be established. The current paper will update the latest progress of HPV infection in several oral potentially malignant disorders and oral squamous cell carcinoma and discuss the impact of HPV infection on the progression of oral potentially malignant disorders.
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Affiliation(s)
- Xun Chen
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, People's Republic of China.
| | - Yu Zhao
- Department of Prosthodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou 510055, People's Republic of China.
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McBride AA. The Promise of Proteomics in the Study of Oncogenic Viruses. Mol Cell Proteomics 2017; 16:S65-S74. [PMID: 28104704 DOI: 10.1074/mcp.o116.065201] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/16/2016] [Indexed: 12/30/2022] Open
Abstract
Oncogenic viruses are responsible for about 15% human cancers. This article explores the promise and challenges of viral proteomics in the study of the oncogenic human DNA viruses, HPV, McPyV, EBV and KSHV. These viruses have coevolved with their hosts and cause persistent infections. Each virus encodes oncoproteins that manipulate key cellular pathways to promote viral replication and evade the host immune response. Viral proteomics can identify cellular pathways perturbed by viral infection, identify cellular proteins that are crucial for viral persistence and oncogenesis, and identify important diagnostic and therapeutic targets.
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Affiliation(s)
- Alison A McBride
- From the ‡Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, 33 North Drive, MSC3209, National Institutes of Health, Bethesda, Maryland 20892
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Liu W, Zeng L, Li N, Wang F, Jiang C, Guo F, Chen X, Su T, Xu C, Zhang S, Fang C. Quantitative proteomic analysis for novel biomarkers of buccal squamous cell carcinoma arising in background of oral submucous fibrosis. BMC Cancer 2016; 16:584. [PMID: 27485544 PMCID: PMC4971621 DOI: 10.1186/s12885-016-2650-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 07/28/2016] [Indexed: 12/28/2022] Open
Abstract
Background In South and Southeast Asian, the majority of buccal squamous cell carcinoma (BSCC) can arise from oral submucous fibrosis (OSF). BSCCs develop in OSF that are often not completely resected, causing local relapse. The aim of our study was to find candidate protein biomarkers to detect OSF and predict prognosis in BSCCs by quantitative proteomics approaches. Methods We compared normal oral mucosa (NBM) and paired biopsies of BSCC and OSF by quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ) to discover proteins with differential expression. Gene Ontology and KEGG networks were analyzed. The prognostic value of biomarkers was evaluated in 94 BSCCs accompanied with OSF. Significant associations were assessed by Kaplan-Meier survival and Cox-proportional hazards analysis. Results In total 30 proteins were identified with significantly different expression (false discovery rate < 0.05) among three tissues. Two consistently upregulated proteins, ANXA4 and FLNA, were validated. The disease-free survival was negatively associated with the expression of ANXA4 (hazard ratio, 3.4; P = 0.000), FLNA (hazard ratio, 2.1; P = 0.000) and their combination (hazard ratio, 8.8; P = 0.002) in BSCCs. Conclusion The present study indicates that iTRAQ quantitative proteomics analysis for tissues of BSCC and OSF is a reliable strategy. A significantly up-regulated ANXA4 and FLNA could be not only candidate biomarkers for BSCC prognosis but also potential targets for its therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2650-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen Liu
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Lijuan Zeng
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Ning Li
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China.
| | - Fei Wang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Feng Guo
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Xinqun Chen
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Tong Su
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Chunjiao Xu
- Department of Oral Medicine, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Shanshan Zhang
- Department of Oral Medicine, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
| | - Changyun Fang
- Department of Oral Medicine, Xiangya Hospital, Central South University, No. 88, Xiangya Road, Changsha, China
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Oral squamous cell carcinoma: Key clinical questions, biomarker discovery, and the role of proteomics. Arch Oral Biol 2016; 63:53-65. [DOI: 10.1016/j.archoralbio.2015.11.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 09/08/2015] [Accepted: 11/20/2015] [Indexed: 12/19/2022]
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11
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Xiao H, Langerman A, Zhang Y, Khalid O, Hu S, Cao CX, Lingen MW, Wong DT. Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery. Oral Oncol 2015; 51:1011-1019. [DOI: 10.1016/j.oraloncology.2015.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 08/11/2015] [Accepted: 08/13/2015] [Indexed: 10/23/2022]
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Proteomic study of HPV-positive head and neck cancers: preliminary results. BIOMED RESEARCH INTERNATIONAL 2014; 2014:430906. [PMID: 24719866 PMCID: PMC3955617 DOI: 10.1155/2014/430906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/20/2014] [Accepted: 01/23/2014] [Indexed: 11/17/2022]
Abstract
Human papillomavirus (HPV) was recently recognized as a new risk factor for head and neck squamous cell carcinoma. For oropharyngeal cancers, an HPV+ status is associated with better prognosis in a subgroup of nonsmokers and nondrinkers. However, HPV infection is also involved in the biology of head and neck carcinoma (HNC) in patients with a history of tobacco use and/or alcohol consumption. Thus, the involvement of HPV infection in HN carcinogenesis remains unclear, and further studies are needed to identify and analyze HPV-specific pathways that are involved in this process. Using a quantitative proteomics-based approach, we compared the protein expression profiles of two HPV+ HNC cell lines and one HPV- HNC cell line. We identified 155 proteins that are differentially expressed (P < 0.01) in these three lines. Among the identified proteins, prostate stem cell antigen (PSCA) was upregulated and eukaryotic elongation factor 1 alpha (EEF1α) was downregulated in the HPV+ cell lines. Immunofluorescence and western blotting analyses confirmed these results. Moreover, PSCA and EEF1 α were differentially expressed in two clinical series of 50 HPV+ and 50 HPV- oral cavity carcinomas. Thus, our study reveals for the first time that PSCA and EEF1 α are associated with the HPV-status, suggesting that these proteins could be involved in HPV-associated carcinogenesis.
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Ohyama Y, Kawamoto Y, Chiba T, Kikuchi K, Sakashita H, Imai K. Differential expression of fatty acid-binding proteins and pathological implications in the progression of tongue carcinoma. Mol Clin Oncol 2013; 2:19-25. [PMID: 24649302 DOI: 10.3892/mco.2013.198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 09/12/2013] [Indexed: 12/16/2022] Open
Abstract
Tongue carcinomas are common malignancies of the oral cavity. Understanding the molecular mechanisms behind the disease progression is a prerequisite for improving patient prognosis. Fatty acid-binding proteins (FABPs) are cytoplasmic lipid chaperones that affect cellular organization and energy production. Although their aberrant expression is involved in carcinoma progression, its role in the pathology of tongue carcinomas remains unclear. In the present study, the immunohistochemical expression of FABP4 and FABP5 in tongue carcinomas (n=58) and its involvement in the clinicopathological parameters were examined. Normal tongue epithelial cells expressed FABP5, an epidermal-type FABP, but not FABP4, an adipocyte-type FABP. The cytoplasmic staining of FABP5 was increased in carcinomas with advanced T-stage (P<0.05) and clinical stage (P<0.05). Ectopic expression of FABP4 was detected in almost all carcinomas, although its role in disease progression remains undetermined. Upregulation of FABP5 in the wounded skin of genetically normal mice indicated that microenvironmental tissue factors induce FABP5 expression. The results of the present study demonstrated the aberrant expression of FABP4 and FABP5 in tongue carcinomas and suggested the involvement of FABP5 in disease progression.
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Affiliation(s)
- Yoshito Ohyama
- Division of Oral and Maxillofacial Surgery 2, Department of Diagnostic and Therapeutic Science, School of Dentistry, Meikai University, Sakado, Saitama 3500283
| | - Yukihiro Kawamoto
- Division of Oral and Maxillofacial Surgery 2, Department of Diagnostic and Therapeutic Science, School of Dentistry, Meikai University, Sakado, Saitama 3500283
| | - Tadashige Chiba
- Department of Biochemistry, School of Life Dentistry at Tokyo, The Nippon Dental University, Tokyo 1028159
| | - Kentaro Kikuchi
- Division of Pathology, Department of Diagnostic and Therapeutic Science, School of Dentistry, Meikai University, Sakado, Saitama 3500283, Japan
| | - Hideaki Sakashita
- Division of Oral and Maxillofacial Surgery 2, Department of Diagnostic and Therapeutic Science, School of Dentistry, Meikai University, Sakado, Saitama 3500283
| | - Kazushi Imai
- Department of Biochemistry, School of Life Dentistry at Tokyo, The Nippon Dental University, Tokyo 1028159
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Seema S, Krishnan M, Harith AK, Sahai K, Iyer SR, Arora V, Tripathi RP. Laser ionization mass spectrometry in oral squamous cell carcinoma. J Oral Pathol Med 2013; 43:471-83. [PMID: 24112294 DOI: 10.1111/jop.12117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2013] [Indexed: 12/15/2022]
Abstract
Biomarker research in oral squamous cell carcinoma (OSCC) aims for screening/early diagnosis and in predicting its recurrence, metastasis and overall prognosis. This article reviews the current molecular perspectives and diagnosis of oral cancer with proteomics using matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI) mass spectrometry (MS). This method shows higher sensitivity, accuracy, reproducibility and ability to handle complex tissues and biological fluid samples. However, the data interpretation tools of contemporary mass spectrometry still warrant further improvement. Based on the data available with laser-based mass spectrometry, biomarkers of OSCC are classified as (i) diagnosis and prognosis, (ii) secretory, (iii) recurrence and metastasis, and (iv) drug targets. Majority of these biomarkers are involved in cell homeostasis and are either physiologic responders or enzymes. Therefore, proteins directly related to tumorigenesis have more diagnostic value. Salivary secretory markers are another group that offers a favourable and easy strategy for non-invasive screening and early diagnosis in oral cancer. Key molecular inter-related pathways in oral carcinogenesis are also intensely researched with software analysis to facilitate targeted drug therapeutics. The review suggested the need for incorporating 'multiple MS or tandem approaches' and focusing on a 'group of biomarkers' instead of single protein entities, for making early diagnosis and treatment for oral cancer a reality.
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Affiliation(s)
- Saraswathy Seema
- Army Base Hospital, School of Medicine & Paramedical Health Sciences, Guru Gobind Singh Indraprastha University, Government of Delhi, Delhi, India
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Leopoldino AM, Squarize CH, Garcia CB, Almeida LO, Pestana CR, Sobral LM, Uyemura SA, Tajara EH, Silvio Gutkind J, Curti C. SET protein accumulates in HNSCC and contributes to cell survival: antioxidant defense, Akt phosphorylation and AVOs acidification. Oral Oncol 2012; 48:1106-13. [PMID: 22739068 DOI: 10.1016/j.oraloncology.2012.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/27/2012] [Accepted: 05/09/2012] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Determination of the SET protein levels in head and neck squamous cell carcinoma (HNSCC) tissue samples and the SET role in cell survival and response to oxidative stress in HNSCC cell lineages. MATERIALS AND METHODS SET protein was analyzed in 372 HNSCC tissue samples by immunohistochemistry using tissue microarray and HNSCC cell lineages. Oxidative stress was induced with the pro-oxidant tert-butylhydroperoxide (50 and 250μM) in the HNSCC HN13 cell lineage either with (siSET) or without (siNC) SET knockdown. Cell viability was evaluated by trypan blue exclusion and annexin V/propidium iodide assays. It was assessed caspase-3 and -9, PARP-1, DNA fragmentation, NM23-H1, SET, Akt and phosphorylated Akt (p-Akt) status. Acidic vesicular organelles (AVOs) were assessed by the acridine orange assay. Glutathione levels and transcripts of antioxidant genes were assayed by fluorometry and real time PCR, respectively. RESULTS SET levels were up-regulated in 97% tumor tissue samples and in HNSCC cell lineages. SiSET in HN13 cells (i) promoted cell death but did not induced caspases, PARP-1 cleavage or DNA fragmentation, and (ii) decreased resistance to death induced by oxidative stress, indicating SET involvement through caspase-independent mechanism. The red fluorescence induced by siSET in HN13 cells in the acridine orange assay suggests SET-dependent prevention of AVOs acidification. NM23-H1 protein was restricted to the cytoplasm of siSET/siNC HN13 cells under oxidative stress, in association with decrease of cleaved SET levels. In the presence of oxidative stress, siNC HN13 cells showed lower GSH antioxidant defense (GSH/GSSG ratio) but higher expression of the antioxidant genes PRDX6, SOD2 and TXN compared to siSET HN13 cells. Still under oxidative stress, p-Akt levels were increased in siNC HN13 cells but not in siSET HN13, indicating its involvement in HN13 cell survival. Similar results for the main SET effects were observed in HN12 and CAL 27 cell lineages, except that HN13 cells were more resistant to death. CONCLUSION SET is potential (i) marker for HNSCC associated with cancer cell resistance and (ii) new target in cancer therapy.
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Affiliation(s)
- Andréia M Leopoldino
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-930 Ribeirão Preto, SP, Brazil.
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Kowalewska M, Radziszewski J, Goryca K, Bujko M, Oczko-Wojciechowska M, Jarzab M, Siedlecki JA, Bidzinski M. Estimation of groin recurrence risk in patients with squamous cell vulvar carcinoma by the assessment of marker gene expression in the lymph nodes. BMC Cancer 2012; 12:223. [PMID: 22673103 PMCID: PMC3414830 DOI: 10.1186/1471-2407-12-223] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 06/06/2012] [Indexed: 01/11/2023] Open
Abstract
Background Regional lymph node (LN) status is a well-known prognostic factor for vulvar carcinoma (VC) patients. Although the reliable LN assessment in VC is crucial, it presents significant diagnostic problems. We aimed to identify specific mRNA markers of VC dissemination in the LN and to address the feasibility of predicting the risk of nodal recurrence by the patterns of gene expression. Methods Sentinel and inguinal LN samples from 20 patients who had undergone surgery for stage T1-3, N0-2, M0 primary vulvar squamous cell carcinoma were analyzed. Gene expression profiles were assessed in four metastatic [LN(+)] and four histologically negative [LN(−)] lymph node samples obtained from four VC patients, by the Affymetrix U133 Plus 2.0 gene expression microarrays. Of the set of genes of the highest expression in the metastatic LNs compared to LN(−), seven candidate marker genes were selected: PERP, S100A8, FABP5, SFN, CA12, JUP and CSTA, and the expression levels of these genes were further analyzed by the real-time reverse transcription polymerase chain reaction (qRT-PCR) in 71 LN samples. Results All of the seven genes in question were significantly increased in LN(+) compared to LN(−) samples. In the initial validation of the seven putative markers of metastatic LN, the Cox proportional hazard model pointed to SFN, CA12 and JUP expression to significantly relate to the time to groin recurrence in VC patients. Conclusions Our findings first provided evidence that SFN, CA12 and JUP have a potential of marker genes for the prediction of the groin recurrence LN in VC patients.
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Affiliation(s)
- Magdalena Kowalewska
- Department of Molecular Biology, Maria Sklodowska-Curie Memorial Cancer Centre, Warsaw, Poland.
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Olthof NC, Straetmans JMJAA, Snoeck R, Ramaekers FCS, Kremer B, Speel EJM. Next-generation treatment strategies for human papillomavirus-related head and neck squamous cell carcinoma: where do we go? Rev Med Virol 2011; 22:88-105. [PMID: 21984561 DOI: 10.1002/rmv.714] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 07/29/2011] [Accepted: 08/08/2011] [Indexed: 12/20/2022]
Abstract
Oncogenic human papillomavirus (HPV) is currently recognised as a major risk factor for the development of head and neck squamous cell carcinomas (HNSCC). HPV is mostly detected in tumours arising from the oropharynx and more specifically from the tonsil. HPV-related tumours display clinical and molecular characteristics that are distinct from HPV-unrelated tumours, which are generally induced by alcohol and tobacco abuse. Detection of biologically active HPV in HNSCC has prognostic relevance, which warrants the separate classification of HPV-induced tumours and is a prerequisite for further optimisation of treatment protocols for this distinct group. Current guidelines for the treatment of oropharyngeal squamous cell carcinoma (OPSCC) have not incorporated specific treatment modalities for HPV-related tumours. The development of such treatment options is still in a preclinical phase or in early clinical trials. Recent data on treatment response of OPSCC have been obtained by retrospectively analysing HPV-status and indicate that patients with HPV-related tumours show a favourable prognosis, independent of the type of treatment. These patients may benefit from de-intensified treatment, which should be assessed in prospective clinical trials. The development and future use of new antiviral and immunomodulatory therapeutics may be instrumental in this approach to improve survival rates and decrease disease-and-treatment-related morbidity. In this review we will focus on present therapeutic HPV-targeting strategies and discuss future directions for de-intensified treatment of HPV-positive HNSCC.
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Affiliation(s)
- Nadine C Olthof
- Departments of Otorhinolaryngology and Head and Neck Surgery, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands.
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Diao L, Clarke CH, Coombes KR, Hamilton SR, Roth J, Mao L, Czerniak B, Baggerly KA, Morris JS, Fung ET, Bast RC. Reproducibility of SELDI Spectra Across Time and Laboratories. Cancer Inform 2011; 10:45-64. [PMID: 21552492 PMCID: PMC3085423 DOI: 10.4137/cin.s6438] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. The reproducibility of mass spectrometry (MS) data collected using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) has been questioned. This investigation was designed to test the reproducibility of SELDI data collected over time by multiple users and instruments. Five laboratories prepared arrays once every week for six weeks. Spectra were collected on separate instruments in the individual laboratories. Additionally, all of the arrays produced each week were rescanned on a single instrument in one laboratory. Lab-to-lab and array-to-array variability in alignment parameters were larger than the variability attributable to running samples during different weeks. The coefficient of variance (CV) in spectrum intensity ranged from 25% at baseline, to 80% in the matrix noise region, to about 50% during the exponential drop from the maximum matrix noise. Before normalization, the median CV of the peak heights was 72% and reduced to about 20% after normalization. Additionally, for the spectra from a common instrument, the CV ranged from 5% at baseline, to 50% in the matrix noise region, to 20% during the drop from the maximum matrix noise. Normalization reduced the variability in peak heights to about 18%. With proper processing methods, SELDI instruments produce spectra containing large numbers of reproducibly located peaks, with consistent heights.
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Affiliation(s)
- Lixia Diao
- Departments of Bioinformatics and Computational Biology
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Li M, Gray W, Zhang H, Chung CH, Billheimer D, Yarbrough WG, Liebler DC, Shyr Y, Slebos RJC. Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling. J Proteome Res 2010; 9:4295-305. [PMID: 20586475 PMCID: PMC2920032 DOI: 10.1021/pr100527g] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography−tandem mass spectrometry (LC−MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. Thus, shotgun proteomics data pose challenges in comparing proteomes from different biological states. We developed an analysis strategy using quasi-likelihood Generalized Linear Modeling (GLM), included in a graphical interface software package (QuasiTel) that reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. This approach was compared to four other statistical analysis strategies: Student t test, Wilcoxon rank test, Fisher’s Exact test, and Poisson-based GLM. We analyzed the performance of these tests to identify differences in protein levels based on spectral counts in a shotgun data set in which equimolar amounts of 48 human proteins were spiked at different levels into whole yeast lysates. Both GLM approaches and the Fisher Exact test performed adequately, each with their unique limitations. We subsequently compared the proteomes of normal tonsil epithelium and HNSCC using this approach and identified 86 proteins with differential spectral counts between normal tonsil epithelium and HNSCC. We selected 18 proteins from this comparison for verification of protein levels between the individual normal and tumor tissues using liquid chromatography−multiple reaction monitoring mass spectrometry (LC−MRM-MS). This analysis confirmed the magnitude and direction of the protein expression differences in all 6 proteins for which reliable data could be obtained. Our analysis demonstrates that shotgun proteomic data sets from different tissue phenotypes are sufficiently rich in quantitative information and that statistically significant differences in proteins spectral counts reflect the underlying biology of the samples. Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes but incomplete sampling poses challenges in comparing protein inventories by spectral counting approaches. We developed a statistical method based on quasi-likelihood modeling and demonstrate that it compares favorably to other statistical tests. Statistically significant spectral count differences were confirmed by MRM demonstrating that the observed protein level differences reflect the underlying biology of the samples.
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Affiliation(s)
- Ming Li
- Department of Biostatistics, Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8575, USA
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Lu Z, Qin A, Qian K, Chen X, Jin W, Zhu Y, Eltahir Y. Proteomic analysis of the host response in the bursa of Fabricius of chickens infected with Marek's disease virus. Virus Res 2010; 153:250-7. [PMID: 20723570 DOI: 10.1016/j.virusres.2010.08.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 08/07/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
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Wu R, Zhao X, Wang Z, Zhou M, Chen Q. Novel Molecular Events in Oral Carcinogenesis via Integrative Approaches. J Dent Res 2010; 90:561-72. [PMID: 20940368 DOI: 10.1177/0022034510383691] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- R.Q. Wu
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec. 3, Renminnan Road, Chengdu, Sichuan, 610041, China
| | - X.F. Zhao
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec. 3, Renminnan Road, Chengdu, Sichuan, 610041, China
| | - Z.Y. Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec. 3, Renminnan Road, Chengdu, Sichuan, 610041, China
| | - M. Zhou
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec. 3, Renminnan Road, Chengdu, Sichuan, 610041, China
| | - Q.M. Chen
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, No. 14, Sec. 3, Renminnan Road, Chengdu, Sichuan, 610041, China
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Robinson M, Sloan P, Shaw R. Refining the diagnosis of oropharyngeal squamous cell carcinoma using human papillomavirus testing. Oral Oncol 2010; 46:492-6. [DOI: 10.1016/j.oraloncology.2010.02.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 02/16/2010] [Accepted: 02/17/2010] [Indexed: 02/08/2023]
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Winkler R. ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:285-94. [PMID: 20049890 DOI: 10.1002/rcm.4384] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open-source GPLv3 license to support future developments of mass spectrometry software.
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Affiliation(s)
- Robert Winkler
- Tecnológico de Monterrey (ITESM), Department of Biotechnology and Food Engineering, Ave. E. Garza Sada 2501-Sur, Monterrey, N.L. Mexico, CP 64849.
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Braakhuis BJ, Brakenhoff RH, Meijer CJ, Snijders PJ, Leemans CR. Human papilloma virus in head and neck cancer: The need for a standardised assay to assess the full clinical importance. Eur J Cancer 2009; 45:2935-9. [DOI: 10.1016/j.ejca.2009.08.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 08/20/2009] [Accepted: 08/21/2009] [Indexed: 11/28/2022]
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